Gut microbiome of healthy Dutch adults, 500FG cohort
517 stool samples from healthy adult participants in the Netherlands, collected as part of the 500 Functional Genomics (500FG) project, in a cross-sectional design. machine-written summary
517 samples · 517 runs · NL · Adult · 2023 · 7.96 Gbp / sample · cohort Gut dysbiosis associates with cytokine production
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 517 sample values (country) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10425223, PMC10873414 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 1,034 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 469 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 517 | 100% | ||||
| country | 517 | 100% | 517 | |||
| health_condition | 517 | 100% | 517 | |||
| subject_id | 0 | 0% | ||||
| health_condition_detail | 517 | 100% | 517 |
- Gut dysbiosis associates with cytokine production capacity in viral-suppressed people living with HIV. 2023 PMID 37583444 PMC10425223 unsure
- Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses. 2024 PMID 38366085 PMC10873414 unsure
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991 unsure
Archive description
As part of the 500 Functional Genomics (500FG) project, stool samples from 471 healthy adults were subjected to metagenomic shotgun sequencing (one time point per individual).</p><p>The same stool samples were sequenced again in this BioProject as the PRJNA319574. Compared with PRJNA319574, fecal DNA extraction in this BioProject carried out using QIAamp Fast DNA Stool Mini Kit (QIAGEN).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host study.description · “stool samples from 471 healthy adults”
- body site study.description · “stool samples from 471 healthy adults”
- life stage study.description · “471 healthy adults”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33692898 | country | NL | R1 | 0.90 | sample.attr.geo_loc_name | Netherlands |
| SAMN33692898 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN33692898 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
Sequencing
517 runs over 517 samples · mean 7.99 Gbp per run (median 7.96 Gbp, total 4,130.15 Gbp; 517 runs with a base count) · layout PAIRED 517 · platform ILLUMINA 517 · models Illumina HiSeq 2000 (517) · 91% of runs with a Sandpiper profile · first public 2023-04-14
Authors (36)
Zhang Y first · Andreu-Sánchez S · Vadaq N · Wang D · Matzaraki V · van der Heijden WA · Gacesa R · Weersma RK · Zhernakova A · Vandekerckhove L · de Mast Q · Joosten LAB · Netea MG · van der Ven AJAM · Fu J last · Fernández-Pato A first · Sinha T · Gois MFB · Gelderloos-Arends J · Jansen DBH · Kruk M · Jaeger M · Wijmenga C · Harmsen HJM · Kurilshikov A last · Elmassry MM first · Sugihara K · Chankhamjon P · Kim Y · Camacho FR · Wang S · Sugimoto Y · Chatterjee S · Chen LA · Kamada N · Donia MS last
Downloads
PRJNA942468.csv.gz (11.7 KB) · parquet (87.7 KB) — all 517 samples, every field with route and confidence · PRJNA942468_determinations.csv.gz (8.5 KB) — 1,551 evidence rows